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1 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
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2 // all rights reserved. Authored by: Brian Ondov, Todd Treangen,
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3 // Sergey Koren, and Adam Phillippy
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4 //
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5 // See the LICENSE.txt file included with this software for license information.
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6
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7 #ifndef INCLUDED_CommandDistance
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8 #define INCLUDED_CommandDistance
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9
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10 #include "Command.h"
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11 #include "Sketch.h"
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12
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13 namespace mash {
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14
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15 class CommandDistance : public Command
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16 {
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17 public:
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18
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19 struct CompareInput
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20 {
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21 CompareInput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew, const Sketch::Parameters & parametersNew, double maxDistanceNew, double maxPValueNew)
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22 :
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23 sketchRef(sketchRefNew),
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24 sketchQuery(sketchQueryNew),
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25 indexRef(indexRefNew),
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26 indexQuery(indexQueryNew),
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27 pairCount(pairCountNew),
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28 parameters(parametersNew),
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29 maxDistance(maxDistanceNew),
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30 maxPValue(maxPValueNew)
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31 {}
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32
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33 const Sketch & sketchRef;
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34 const Sketch & sketchQuery;
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35
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36 uint64_t indexRef;
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37 uint64_t indexQuery;
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38 uint64_t pairCount;
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39
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40 const Sketch::Parameters & parameters;
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41 double maxDistance;
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42 double maxPValue;
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43 };
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44
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45 struct CompareOutput
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46 {
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47 CompareOutput(const Sketch & sketchRefNew, const Sketch & sketchQueryNew, uint64_t indexRefNew, uint64_t indexQueryNew, uint64_t pairCountNew)
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48 :
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49 sketchRef(sketchRefNew),
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50 sketchQuery(sketchQueryNew),
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51 indexRef(indexRefNew),
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52 indexQuery(indexQueryNew),
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53 pairCount(pairCountNew)
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54 {
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55 pairs = new PairOutput[pairCount];
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56 }
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57
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58 ~CompareOutput()
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59 {
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60 delete [] pairs;
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61 }
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62
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63 struct PairOutput
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64 {
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65 uint64_t numer;
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66 uint64_t denom;
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67 double distance;
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68 double pValue;
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69 bool pass;
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70 };
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71
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72 const Sketch & sketchRef;
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73 const Sketch & sketchQuery;
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74
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75 uint64_t indexRef;
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76 uint64_t indexQuery;
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77 uint64_t pairCount;
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78
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79 PairOutput * pairs;
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80 };
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81
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82 CommandDistance();
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83
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84 int run() const; // override
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85
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86 private:
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87
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88 void writeOutput(CompareOutput * output, bool table, bool comment) const;
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89 };
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90
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91 CommandDistance::CompareOutput * compare(CommandDistance::CompareInput * input);
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92 void compareSketches(CommandDistance::CompareOutput::PairOutput * output, const Sketch::Reference & refRef, const Sketch::Reference & refQry, uint64_t sketchSize, int kmerSize, double kmerSpace, double maxDistance, double maxPValue);
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93 double pValue(uint64_t x, uint64_t lengthRef, uint64_t lengthQuery, double kmerSpace, uint64_t sketchSize);
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94
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95 } // namespace mash
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96
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97 #endif
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